First off, what is the age of your rider? The KTM Pro Jr. or Cobra Jr. is for the 4-6 class and the Pro Sr. is for the 7-8yr olds. If you plan on running AMA events, get the bike that is for your rider's age group.
We ran KTM's in the PeeWee's and had friends that rode Cobra's. Not a lot of differences, except personal taste. Find some PeeWee parents that have a KTM and Cobra and see if they will let your rider try them. Then buy whichever one they like best and feel more confident with. Getting the one that your rider likes will be more important than what everyone might recommended. The more confident your rider feels, usually the better they will progress and enjoy. As was already mentioned, if you do go with the KTM's,
www.ktmtalk.com has a separate forum for just the 50's. There is a lot of usefull information on setup and maintenance there. So take advantage of it.
Reliability on either one is dependent upon the rider (if they blip the throttle a lot, it's hard on the clutches) and Dad's willingness to spend time in the garage maintaining them.
I don't know why a lot of people think getting KTM parts is a problem. Holeshot in Akron does a great job on stocking parts. They only sell KTM's. There are numerous KTM only dealers that have webstores, like MunnRacing and Cycle Hutt. Both have a good supply of parts in their inventory. Avoid Dealers that sell Jap bikes, quads, etc.... plus KTM's as they just can't afford to stock a lot of parts. Thus they have to order nearly everything.
Which everone you decided on, get your spare parts with the bike. This would be items like clutch dics, clutch springs, xtra piston & rings, etc... and keep them in the garage or trailer on race day. Don't wait for the bike to break, then order parts.
Probably the best advise is if your rider is 6 or 7yrs old, pick up a 65 and get them on it. Less maintenance and overall operating cost. In the long run, cutting the PeeWee years short a season or two and having them on a 65 will same Mom & Dad a lot of stress as the 50 racing bikes require a lot of attention if they're being raced every weekend.
Good Luck